Halfa Cure
by PhantomWorks- Stories division
Summary: It is funny how a few small changes can change the entire world a path I closed of decades ago leads to a disaster where salvation is stolen and then lied about while this new path creates a win for everyone. I am Clockwork but this isn't my story, it is the story of 2 young teens whose completely separate lives a combined by one simple accident. I Own Nothing!
1. Chapter 1 the portal accident

**Hi guys. This idea just came to me today. In this story the fungus that is responsible for the infection is killed by the radiation of ectoplasm and the Fenton's live in Boston and finished the portal in 2013, the day of the evacuation and 6 years prior to Danny, and Ellie's births. Also we continue with my theory that Ellie is in fact bisexual because in this story I am pairing her with Danny, which is weird considering that in my other last of us story she is paired, or will be, with Danny's clone/daughter Danielle. Please give better suggestions for a title I am fairly good with plots but no so good with titles. The story starts somewhen between when Joel, Tess and Ellie encounter the soldiers and Ellie's immunity is revealed and the eventual arrival at city hall where Tess reveals her infection.**

**Also if you are curious it May be the apocalypse but Jack and Maddie, prior to forced enlistment to outside duty, were still geniuses who homeschooled their son and I always liked genius Danny. They made his tech over the 14 years of his life.**

**See the end note for 3 plot bunnies.**

_**Chapter 1 the portal accident**_

"No. Nonononononononononono. NO!" this was what Daniel Fenton said to himself as he stood in the lab his parents had built staring at the bite mark on his hand. After everything he had done one infected got a lucky bite and it was all for nothing.

"I can't believe that after all this work this is how it ends? NO!" In complete disbelief he starts angrily muttering as he walked into the large heptagonal tunnel in the side of the room, his parent's greatest invention.

20 years ago Danny's parents were paranormal scientists and inventors and had constructed a portal to the ghost zone, a powerful device capable of punching a hole into the parallel dimension where ghosts live, but then the infection rose and the world descended into chaos and they had to move to the quarantine zone. They were able to take or recreate a lot of their technology and even allow their young son to invent his own gear, but they couldn't move or rebuild the portal. Ever since he heard about it Danny knew what he needed to do. He needed to head to the portal and activate it.

He had got his chance when his family was selected for 'outside work' once he was alone he snuck out and used a smugglers tunnel and his cyber mask (Peter quill's mask from guardians of the galaxy with blue **(Green in ghost mode) **eyes) he made it out of the quarantine zone. He had nearly made it to the lab but he was ambushed buy a pack of runners. He took them down and fell into the lab at the same time but one got lucky. The bite was comparatively small. But it was a bit and that was enough.

* * *

Ellie was a 14 year old girl with some strange immunity to the infection. She had learnt this 3 weeks ago when she and her best friend Reilly had been ambushed and bitten in a mall by a group of runners.

She wore blue jeans and a black long sleeve shirt and a red T-Shirt with a tropical sunset on the chest. She had green eyes and reddy brown hair. She was wearing a blue rucksack. Close behind her were Joel and Tess 2 smugglers the fireflies had hired to take her to a group at the capitol building.

Unbeknownst to the others Tess had been infected about ¼ of an hour ago so was only up to 2 days away from becoming a runner.

Joel was still quite foul tempered, having not spent time around children, particularly young teenagers like Ellie, since the start of the infection 20 years ago when his 12 year old daughter was shot dead for no reason by a soldier on night one of this horror story.

Ellie was the suddenly furrowed her eyebrows, hearing something, muttering, not the sounds infected made but a person talking under their breath. Curious she strayed over to the hole it was coming from when the floor beneath her feet collapsed. She shrieked, alerting the 2 smugglers but before they could run forward they saw a pack of runners and a clicker heading towards the hole.

Unaware of the impending doom Ellie stood up to find herself in a small lab. In front of her she could see a tunnel with a teenage boy sat at the end muttering to himself.

"Hey! You all right?" she called walking into the chamber before tripping on a wire and falling, hitting a wall hard as she fell. Suddenly she heard a click before a steady whirring sound. She and the boy got to their feet and were about to run when the group of infected fell down.

"S***." Was all Ellie could manage before the chamber was filled with green energy that wasted no time in leaking out into the lab. The 2 teens let out horrific screams of pain.

Then the device sparked and blew up.

When the lights died down Joel and Tess ran over to the edge to see their charge and the teen unconscious among a sea of corpses.

Jumping down Joel noticed he couldn't identify the clicker. Confused he scanned the group even the 2 teens.

"Holy S***!" he exclaimed, showing Tess the scanner, which he had stolen from the soldiers that held them up earlier. Having scanned a group that contained a maximum of 1 uninfected being it was registering absolutely zero fungal infection.

* * *

**And that was chapter one. Yes it is short but we will get longer in the future, hopefully. Also though Danny is smart now in Wyoming both he and Ellie will get a lot smarter.**

**This chapter was, as the title suggests simply a set up for the accident and the hints of the portal accident's anti fungal effect.**

**Onto the plot bunnies.**

**#1 a Danny Phantom and The Last of Us crossover (I am the only one contributing to this category right now!)**

**Basic plot: Ellie gets caught in a natural ghost portal and lighting accident that not only turns her Halfa (With the same effect as here) but sends her hurtling into the Danny Phantom dimension in amity park.**

**It's up to you if who you want to pair her with but basically work from there.**

**#2 basically a near reverse of #1**

**Danny (Immune like in this story for the same reason) somehow winds up in the last of us universe and winds up alongside Joel and Ellie.**

**Try to have it set some time early into the game; heck you could even have it that Danny is already with Ellie or Joel at the start of the main game (After the flashback) and work from there if you want!**

**#3 a transformers and the last of us crossover.**

**Plot: set in a similar post DOTM setting as AOE cemetery wind and KSI a destroyed by the infection after it is reduced to just the dirty foursome and Optimus. Lockdown abandons the planet, though infected cause the ship the Dinobots are on to crash off, and he flies off, explaining that any transformers still on planet are as good as dead. Optimus was far less wounded taking on his first AOE form; simply deactivating himself to avoid detection. 20 years later he winds up in Lincoln where he is nearly fully fixed up by Frank (Bill's partner) and is finally reactivated by Ellie, Joel and Bill. In the face of this battle Optimus is convinced to help them because of Ellie, a young person who is yet to actually take a life.**

**You can decide how the plot is changed by Joel and Ellie having Optimus instead of a pickup (Naturally the hunter's trap will be less effective) and if the other autobots will make an appearance but (for logical reasons) drift and crosshairs will need new alt forms (Optimus' evasion mode, Bumblebee's high octane mode, and hound's altforms would look less out of place in this setting).**

**I may actually attempt #3 myself.**

**Anyway next chapter we will see Danny and Ellie waking up and more explanations. See you there!**


	2. Chapter 2 something new

**And here's chapter 2. This will feature the awakening of our 2 new Halfas and the revelation that the accident cured them, and immunised them.**

_**Chapter 2 something ... new**_

Joel and Tess looked at Ellie and the boy. They didn't look the same as they used to.

Ellie now had a darker black shirt and her pants. Backpack and T-Shirt had turned black with green stitching. Her T-Shirt and backpack were both branded with white EP insignias. Her shoes were white with green stitching and laces. Her hair was now pure white.

The boy was wearing black cargo pants with green stitching and a black T-Shirt with green stitching and a white DP insignia. He was wearing a black light jacket with a black rucksack sewed in with green thread. It too was branded with the DP logo. He also had a white fingerless glove with black stitching on one hand; the other glove seemed to be in his pocket. He had the same white hair as Ellie. And white trainers with black highlights and green stitching. He was wearing a DP branded wristwatch and a chain coming from a belt loop, where he had a white belt, to a black pocket watch.

The boy had a bite mark on his bare palm and Ellie's was exposed because her sleeve had been pulled up.

"Joel look." Tess said; breathless. It was known that fungal growth was seen almost instantly but not only was there no fungal growth but the bites were sealing up, leaving unbroken skin.

"Oh my god." Joel said.

Suddenly a white ring appeared around the 2 teens' waists and turned them back to normal. Ellie look just like she had as long as they had known her but without the bite mark. The boy now had black hair and black trainers. His glove and belt was black and his pants were dark blue. His jacket was a light green-brown. His shirt was white with red highlights and a red oval on the chest.

Their eyes opened, the boy's eyes being revealed as light blue.

The teen brought his hand into his eye line and his eyes widened at seeing no bite.

"What the? Where's my bite mark? I can't even feel the infection." He said.

"That's because whatever just happened cured you." Joel said. Ellie, having also awakened, looked at her mark.

"Holy S***!" She exclaimed as she stared at her arm. "My bite's gone!"

"What happened?" Joel asked.

"Well that thing over there." Gesturing to the portal. "Was made by my parents. They finished it right before the outbreak and I wanted to finally activate it. My parents had outside duty and I used a smuggler tunnel. I was attacked by a pack of runners and was bitten. I took them out though. I was sulking in the portal when your friend and that pack of infected fell down here. She tripped and hit the old on switch. We must have been caught in the charge up sequence and the damaged portal must have bathed the infected in ecto radiation."

"Ecto. You mean ghost energy?" Ellie said.

"Yeah. It is a _ghost_ portal." Danny said sarcastically.

"Regardless, what does this mean?" Joel asked.

"I think the fungus May be extremely sensitive to ecto radiation." Danny said. "Wait I've got an idea!" he drew some blood from his arm and activated his mask. He walked up stairs and walked over to a fungal growth. Once there he emptied the blood onto the fungus. It immediately started to melt.

"As I thought." He muttered.

"What?" Ellie asked, running over.

"I theorized that, if exposed to enough ectoplasmic energy mixed with electricity it would turn you into a hybrid of human and ghost called a Halfa, the thing is if you don't get a full body blast then the unaffected parts of you will suffer ecto radiation poising from the radiation our blood emits. It disperses instantly but if you come into direct contact, nasty." Joel looked up as the teen explained all this.

"So we have a confirmed cure?" he asked. The boy sighed.

"Yes and no. Firstly we need to project the energy across the entire planet to prevent reinfection, secondly we would need to set it lower, I can feel a lot of power inside myself, I have a feeling you know what would happen if some people got their hands on that power. I don't know how to arrange that yet and I have no resources here." He said.

"Maybe if we explain it to the fireflies they can help." Ellie suggested.

"It could work." Tess said.

"Sure." Joel said. "Hey where'd you get that mask?"

"My parents were inventors and I inherited that trait." He pulled on his over glove and got out a device extremely similar to a smart phone. "This is my pod. It is a personal super computer. It can shift to hand held, tablet and desktop mode as well as produce 3D projections." He said. Then he tapped on his watch. A round shield formed from translucent energy. "My watch creates a shield that an reconfigure into numerous forms to help me out." The 4 robotic arms snaked out from his back. "And my shirt has a harness built into it that gives me these 4 mechanical arms that I can use to do things I May not be able to with my own arms. I also have a nanotech chip in the back of my neck. It helps me to mentally control my gear. The mask, when out acts as a divers mask and HUD allowing sight from the end of my mechanical arms. I could fix up some for you guys at the next stop." He offered.

"Awesome!" Ellie exclaimed before frowning. "What's your name?" Joel and Tess were roused from their stupor realising they had forgotten to ask the boy his name.

"Danny. Danny Fenton." The now identified Danny said. Joel's eyes widened, the Fentons where one of the few who kept their surnames.

"Cool. I'm Ellie, this is Tess and that's Joel." Ellie said.

* * *

A few minutes after they had gotten out of the lab the group got to a flooded area around the capitol building. Ellie looked nervous.

"Uh not to alarm anyone, but I can't swim." Ellie said nervously.

"It doesn't look that deep. You should be fine." Joel said as they walked through the area.

"When we get a chance I will teach you." Danny said. As they opened the door.

"Thanks." Ellie smiled.

"No, no, no!" Tess exclaimed. Looking the to teens saw that Tess was stood over 2 dead fireflies.

Tess was searching through the packs.

"Where was the lab? Where were they supposed to take you?"

"I don't know they never said." Ellie said.

"Why?" Danny asked.

"Because we need to get her to them. Take her to Tommy's Joel. Please." She begged.

"Why, why are you so desperate?" he asked.

"Because it can't be for nothing." Danny said softly in realisation.

"She's infected." Ellie said in realisation.

"What? How can you tell?" Joel exclaimed.

"Because she is reacting with the same desperation as me when I was bit." Danny said with Ellie nodding.

"Tess?" Joel asked.

She pulled her shirt aside to show a nasty looking bite mark. "Oops? Right?" she said. She pointed over to the 2 14 year olds. "She was infected for 3 weeks and it wasn't as bad as a bite I got an hour ago. We saw him be completely cleansed of infection! A syringe of blood destroyed a fungus pod! This is f***ing real Joel! You need to save these kids, please. If our time together meant anything at all then get these kids to Tommy's." She was practically hysterical now. She turned to Danny. "You took out a pack of runners. Promise me you will protect them. Please!"

"Halfa's honour." He said.

"Go. I'll hold off the military. You get them to safety. Please. Make this easy for me." She pleaded.

"I'm sorry." Danny said as the trio walked over to the stairwell.

* * *

**And that's a wrap. In the next chapter we will see a little more Danny/Ellie and the subway segment. If Danny doesn't seem as effected it's because he knew her for a maximum of 20 minutes. Ellie knew her for about a day and Joel knew her for years. Next time we will time skip to the subway.**


	3. Chapter 3 fallout Boston subway?

**And I'm back. If I haven't posted it already I have written a chapter of my transformers challenge titled 'the last Prime of us' but whatever. Also for note neither this nor that will follow the Pittsburgh threat because though I like how they pulled it off I don't have the heart to write in Henry and Sam when anyone who isn't simply doing what I did a few weeks ago and picking random crossover categories to read and actually knows the story would be able to state the tragic fate they suffer, I also am in the midst of a marvel/last of us/Phantom/doctor who at least brainstorming phase. It would feature the timelord 2.0 ultimate Phantom and a post last of us world. Also in this story some time between bill and Tommy, which will feature more Danny/Ellie bonding (By the time they reach Tommy they will be official) and Halfa training, we will see Danny produce a Phantom suit variant based on the HTTYD2 Hiccup armour. Also I will feature marvel with Shadowcat, Nightcrawler and mutant versions of Spider Man and Silk (ASM vol 3) at Tommy's camp.**

**Regardless down here we will start in the sewers.**

_**Chapter 3 fallout... Boston subway?**_

Joel put on his gas mask as he entered the spore filled subway station. Behind him was Danny in his mask (For the HUD and to assist in breathing and Ellie in some of Danny's old goggles for visibility. Ellie was a bit in shock, not only having just abandoned Tess but also having seen Joel's brutal side, having gone as far as to get 2 soldiers with a Molotov cocktail **(In their remastered walkthrough TheMediaCows actually did this here)**, and as such was uncharacteristically quiet.

In total silence and synchronism Joel and Danny came up behind the 2 men patrolling the subway and snapped their necks. Looking at the 2 Ellie saw different things. Joel was cleanly simply accepting that it was the soldiers or them and it scared Ellie that this was a not uncommon attitude, Danny looked sad at what needed to be done. If the soldiers remained active they would see them and if they saw them Joel would be killed, Danny and Ellie were unsure if death was even an option for them, and they would have no way to get to where they could administer the cure.

Then they walked up to the tracks. They were only a few hundred yards from where they needed to get out but it was through a flooded tunnel.

"Um I still can't swim." Ellie pointed out.

"Can you hold on?" Danny asked.

"Yes?" Ellie replied.

"Then hold on to me and I'll swim for you."

"You can swim?" Joel asked.

"Yeah, my parents taught me."

Either way Danny and Joel started swimming with Ellie clinging to Danny's neck. When they got in place Danny allowed a pair of robot arms to slide up, weaving past Ellie and pull the 2 of them up before grabbing Joel by the backpack. They then started walking down the maintenance tunnel and out into the wilderness.

"Look, about Tess-" Ellie started before Joel cut her off.

"Here's how things are goanna work. You don't bring up Tess, ever, in fact if you 2 want to share histories then fine but leave me out of it." He snapped.

"If it helps you have my condolences too." Danny said. In the brief time they had been alone together Danny had noticed that Joel was harder on Ellie than on him or Tess. This suggested that he had a problem with girls around his age. He had an idea about it but wasn't going to bring it up for now. "Now what?" he asked, a hint of bitterness in his voice.

"I have a friend, well contact, who owes me and Tess some favours. He can get us a car and we can work from there." Joel said.

"Fine." Danny and Ellie said together. Danny also noted with mild curiosity that he was tasting hurt that definitely wasn't his. Ellie to was felling someone else's anger and looking at each other they saw these emotions on each others face as they melted into shocked confusion and they heard each other think.

'_No way.'_

* * *

"So what are you saying?" Ellie said as they walked behind Joel, marvelling at a nature they had never seen before.

"Well we were both in the portal when it activated. I think that somehow as we were remade as Halfas our sols were intertwined, creating a psychic link between one and other. That's how we were able to feel each other's emotions and thoughts. If we practice we may be able to have a private link for communication." Danny explained.

Ellie then looked ahead and laughed, running up to a group of fireflies. "Hey look fireflies, real fireflies that is." Danny chuckled, though also interested in the glowing insects and came over to the girl; Joel tried to be annoyed but couldn't suppress a small smile at the 2 quite mature teen's quite innocent fascination.

Joel meanwhile used a plank to build a bridge over the fence that was blocking their way into Lincoln. He spotted some smoke. "That you Bill?"

"Where do you guys meet up normally?" Danny asked.

"Um... different places." Joel replied absently.

"You've never been here before have you?" Ellie chuckled.

"No. I know he lives here but no I've never actually been here personally." Joel admitted.

"So the smoke is our best bet at finding him?" Danny asked.

"Yes."

"Then let's go." Danny and Ellie said together.

* * *

**And that's a wrap for chapter 3 of the Halfa cure. In this chapter we learn that Danny and Ellie developed a psychic link in the accident but over wise no Halfa development they also have yet to achieve ghost mode. This will happen, alongside 2 of the main 3 (Invisibility and intangibility leaving flight for later) and ecto blasts. Next chapter will have the exploration of Lincoln and the meeting with Bill. It will also probably be the emergence of Phantom and Spectre (Ellie's ghost mode). Also up soon should be chapter one of the last Prime of us. See you later.**


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